Analysis of the algorithm: From rankings to backup genes.
Ranking section
For each of the affected genes present in the list, a ranking with the score and percentile of every possible gene was obtained.
Once this was done, the position for every known backup gene was obtained and the statistical descriptor of all the values calculated.
Table 1. Backup position values for every kernel and net before integration.
| Net |
Kernel |
Elements |
Min |
Max |
Average |
Standard_Deviation |
| biological_process |
ct |
12 |
0.0 |
0.559 |
0.156 |
0.147 |
| biological_process |
el |
12 |
0.235 |
0.955 |
0.73 |
0.237 |
| biological_process |
ka |
12 |
0.0 |
0.591 |
0.137 |
0.158 |
| biological_process |
rf |
12 |
0.0 |
0.559 |
0.156 |
0.147 |
| cellular_component |
ct |
12 |
0.001 |
0.535 |
0.2 |
0.166 |
| cellular_component |
el |
12 |
0.052 |
0.893 |
0.441 |
0.31 |
| cellular_component |
ka |
12 |
0.002 |
0.547 |
0.2 |
0.167 |
| cellular_component |
rf |
12 |
0.0 |
0.535 |
0.2 |
0.166 |
| disease |
ct |
5 |
0.002 |
0.945 |
0.32 |
0.398 |
| disease |
el |
5 |
0.013 |
0.764 |
0.39 |
0.307 |
| disease |
ka |
5 |
0.0 |
0.618 |
0.241 |
0.284 |
| disease |
rf |
5 |
0.002 |
0.934 |
0.317 |
0.394 |
| genetic_interaction |
ct |
8 |
0.017 |
0.954 |
0.506 |
0.29 |
| genetic_interaction |
el |
8 |
0.018 |
0.814 |
0.489 |
0.265 |
| genetic_interaction |
ka |
8 |
0.001 |
0.009 |
0.004 |
0.003 |
| genetic_interaction |
rf |
8 |
0.017 |
0.936 |
0.5 |
0.283 |
| molecular_function |
ct |
12 |
0.0 |
0.832 |
0.331 |
0.277 |
| molecular_function |
el |
12 |
0.178 |
0.785 |
0.459 |
0.177 |
| molecular_function |
ka |
12 |
0.0 |
0.817 |
0.304 |
0.271 |
| molecular_function |
rf |
12 |
0.0 |
0.832 |
0.327 |
0.275 |
| pathway |
ct |
3 |
0.055 |
0.202 |
0.123 |
0.06 |
| pathway |
el |
3 |
0.002 |
0.151 |
0.092 |
0.065 |
| pathway |
ka |
3 |
0.002 |
0.127 |
0.059 |
0.051 |
| pathway |
rf |
3 |
0.037 |
0.157 |
0.088 |
0.051 |
| phenotype |
ct |
5 |
0.001 |
0.234 |
0.08 |
0.093 |
| phenotype |
el |
5 |
0.273 |
0.763 |
0.591 |
0.179 |
| phenotype |
ka |
5 |
0.001 |
0.244 |
0.109 |
0.095 |
| phenotype |
rf |
5 |
0.001 |
0.234 |
0.08 |
0.093 |
| protein_interaction |
ct |
12 |
0.0 |
0.349 |
0.067 |
0.108 |
| protein_interaction |
el |
12 |
0.0 |
0.39 |
0.058 |
0.107 |
| protein_interaction |
ka |
12 |
0.0 |
0.032 |
0.006 |
0.009 |
| protein_interaction |
rf |
12 |
0.0 |
0.325 |
0.065 |
0.104 |
Table 2. Backup position values for every kernel after integration
| Integration |
Kernel |
Elements |
Min |
Max |
Average |
Standard_Deviation |
| integration_mean_by_presence |
ct |
12 |
0.0 |
0.775 |
0.284 |
0.226 |
| integration_mean_by_presence |
el |
12 |
0.01 |
0.759 |
0.28 |
0.221 |
| integration_mean_by_presence |
ka |
12 |
0.0 |
0.724 |
0.193 |
0.21 |
| integration_mean_by_presence |
rf |
12 |
0.001 |
0.329 |
0.056 |
0.091 |
| mean |
ct |
12 |
0.0 |
0.724 |
0.24 |
0.246 |
| mean |
el |
12 |
0.001 |
0.5 |
0.182 |
0.152 |
| mean |
ka |
12 |
0.0 |
0.345 |
0.128 |
0.128 |
| mean |
rf |
12 |
0.001 |
0.328 |
0.054 |
0.09 |
CDF plots of non integrated kernels
CDF plots of integrated kernels